Contacts of the helix formed by residues 231 - 249 (chain B) in PDB entry 2QNJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B VAL* 3.7 19.3 - - - +
230B ASP* 1.3 80.4 - - - +
232B PRO* 1.3 77.1 - - - +
233B GLU* 3.1 11.1 + - - -
234B VAL* 3.2 17.3 + - - +
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Residues in contact with PRO 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 3.6 36.6 - - + +
175B VAL* 4.0 18.3 - - + -
231B GLY* 1.3 82.5 - - - +
233B GLU* 1.3 77.7 + - - +
234B VAL 3.0 0.4 - - - -
235B ASP* 3.0 15.2 + - - +
236B VAL* 3.0 17.5 + - + +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLU* 4.7 1.3 - - - +
230B ASP 4.1 3.4 - - - +
231B GLY* 3.2 20.8 - - - -
232B PRO* 1.3 84.8 - - - +
234B VAL* 1.3 62.0 + - + +
236B VAL* 3.4 10.6 - - - +
237B TRP 3.1 16.8 + - - -
292B PRO* 3.6 41.5 - - + +
293B ILE* 5.2 6.1 - - + +
295B ARG* 3.2 17.1 + - + +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 4.2 18.6 - - + +
220B ALA* 4.4 3.3 - - + +
222B GLU* 3.9 19.1 - - - +
228B LYS 5.5 0.2 - - - +
229B TYR* 3.6 51.6 - - + +
230B ASP* 3.5 20.9 - - - +
231B GLY 3.4 14.8 - - - +
232B PRO 3.0 0.2 + - - -
233B GLU* 1.3 72.7 - - + +
235B ASP* 1.3 68.8 + - - +
237B TRP* 3.0 15.1 + - - +
238B SER* 3.1 17.6 + - - +
295B ARG* 4.4 1.3 - - - +
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 4.5 6.7 - - + -
170B HIS* 2.8 30.5 + - + +
175B VAL* 3.4 8.7 - - - +
176B HIS 3.4 17.7 + - - -
177B ARG* 2.9 29.8 + - - -
179B LEU* 3.2 21.6 - - + +
197B PHE* 3.5 9.6 - - - -
232B PRO 3.0 8.6 + - - +
234B VAL* 1.3 79.8 - - - +
236B VAL* 1.3 63.5 + - - +
238B SER* 2.9 6.1 + - - -
239B LEU* 2.9 26.7 + - + +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 4.8 3.6 - - + +
232B PRO* 3.0 21.8 + - + +
233B GLU* 3.4 11.9 - - - +
235B ASP* 1.3 73.7 - - - +
237B TRP* 1.3 64.9 + - - +
239B LEU* 3.0 13.6 + - - +
287B PHE* 3.1 50.9 - - + +
295B ARG* 4.4 10.1 - - + +
296B GLY 3.5 25.6 - - - +
297B THR* 5.0 1.6 - - - -
298B LEU* 3.9 27.4 - - + +
301B ILE* 4.4 1.1 - - + -
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PRO 5.2 0.4 + - - -
218B TYR 3.6 9.6 - - - -
219B ALA 3.3 15.3 + - - -
220B ALA* 3.5 26.2 - - + -
221B PRO* 3.4 31.0 - - + -
233B GLU 3.1 6.1 + - - -
234B VAL 3.0 10.8 + - - +
236B VAL* 1.3 76.7 - - - +
238B SER* 1.3 66.5 + - - +
240B GLY 3.1 8.3 + - - -
241B VAL* 3.2 22.7 + - + +
253B PHE* 3.4 38.0 - + - -
265B VAL* 4.4 15.5 - - + -
268B GLY* 4.9 2.0 - - - -
287B PHE 4.1 9.4 - - - -
288B LEU* 3.5 36.0 - - + +
289B VAL 3.4 19.7 - - - -
290B LEU* 4.2 7.0 - - + -
295B ARG* 3.4 21.2 - - - +
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Residues in contact with SER 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.6 38.4 - - - +
218B TYR* 2.9 29.3 + - - -
219B ALA* 5.1 0.2 - - - -
229B TYR* 5.5 0.2 + - - -
234B VAL* 3.1 15.1 + - - +
235B ASP 2.9 8.3 + - - -
237B TRP* 1.3 78.2 - - - +
239B LEU* 1.3 57.2 + - - +
241B VAL* 3.2 8.8 + - - +
242B ILE* 2.9 31.0 + - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 3.3 12.5 - - + -
162B ILE* 4.0 26.0 - - + -
163B VAL* 4.1 23.8 - - + -
166B VAL* 3.9 35.4 - - + -
179B LEU* 5.0 7.2 - - + -
235B ASP* 2.9 20.5 + - + +
236B VAL* 3.0 8.9 + - - +
238B SER* 1.3 76.4 - - - +
240B GLY* 1.3 60.3 - - - +
242B ILE* 3.0 19.5 + - + +
243B LEU 2.8 24.9 + - - -
287B PHE* 3.7 11.0 - - + -
298B LEU* 4.1 13.9 - - + -
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL 3.1 6.7 + - - -
237B TRP 3.1 6.2 + - - -
239B LEU* 1.3 74.6 - - - +
241B VAL* 1.3 62.4 + - - +
243B LEU* 3.2 7.3 - - - +
244B TYR* 3.0 18.4 + - - +
284B LEU* 3.4 9.8 - - - +
287B PHE* 3.3 33.7 - - - -
288B LEU* 3.7 9.6 - - - -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PRO 3.8 22.4 - - - +
218B TYR* 3.8 22.2 - - + -
237B TRP* 3.2 38.9 + - + +
238B SER* 3.2 9.6 + - - +
240B GLY* 1.3 74.4 - - - +
242B ILE* 1.3 62.7 + - - +
244B TYR* 3.2 5.4 + - - +
245B THR* 3.1 20.6 + - - +
251B LEU* 4.7 5.6 - - + -
252B PRO* 3.7 32.3 - - + -
253B PHE* 4.5 2.9 - - + -
288B LEU* 3.7 7.3 - - + +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 6.1 0.7 - - + -
159B PHE* 4.4 4.7 - - + -
162B ILE* 4.2 17.5 - - + -
179B LEU* 4.8 12.1 - - + -
180B LYS 5.9 2.0 - - - +
184B LEU* 3.6 43.1 - - + -
218B TYR* 3.8 22.0 - - + -
238B SER 2.9 23.8 + - - +
239B LEU* 3.0 23.8 + - + +
241B VAL* 1.3 74.7 - - - +
243B LEU* 1.3 64.2 + - - +
245B THR* 2.7 27.3 + - - +
246B LEU* 3.1 15.9 + - + +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 3.6 31.7 - - + -
239B LEU 2.8 11.7 + - - +
240B GLY 3.2 10.5 - - - +
242B ILE* 1.3 73.9 - - - +
244B TYR* 1.3 64.4 + - - +
246B LEU* 3.0 17.3 + - + +
247B VAL* 3.2 22.9 + - + +
280B CYS* 4.6 8.1 - - - -
283B LEU* 3.7 33.0 - - + -
284B LEU* 3.7 24.5 - - + +
287B PHE* 4.6 3.6 - - + -
306B TRP* 4.0 26.5 - - + -
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Residues in contact with TYR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLY 3.0 9.0 + - - +
241B VAL 3.3 9.6 - - - +
243B LEU* 1.3 80.3 - - - +
245B THR* 1.3 56.9 + - - +
247B VAL* 3.8 5.1 - - - +
248B SER* 2.9 53.9 + - - -
250B SER* 3.2 25.1 - - - -
251B LEU 4.1 3.8 - - - -
252B PRO* 3.5 39.4 - - + +
270B TYR* 3.8 18.2 - + + -
271B ARG* 2.5 44.9 + - - +
273B PRO* 3.9 6.4 - - + +
276B MET* 4.0 13.0 - - + -
284B LEU* 3.8 23.5 - - + +
288B LEU* 5.4 0.9 - - + -
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Residues in contact with THR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 5.6 0.7 - - - +
141B PHE* 3.9 15.2 - - + -
144B LEU* 3.5 24.6 - - - +
218B TYR* 4.4 6.6 + - - +
241B VAL* 3.1 14.3 + - + +
242B ILE* 2.7 24.6 + - - +
244B TYR* 1.3 76.4 - - - +
246B LEU* 1.3 60.0 + - - +
249B GLY* 2.8 28.2 + - - -
250B SER 3.2 21.1 - - - +
251B LEU* 3.8 26.9 - - + -
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 3.7 29.6 - - + -
144B LEU* 4.2 7.5 - - + +
149B ARG* 4.0 0.7 - - - -
150B MET* 3.0 52.8 + - + +
155B ALA* 4.1 28.7 - - + +
158B LYS* 4.6 6.1 - - + -
159B PHE* 3.9 32.3 - - + +
162B ILE* 4.2 13.9 - - + -
192B ILE* 5.9 0.4 - - + -
242B ILE* 3.1 16.1 + - + +
243B LEU* 3.0 9.7 + - + +
245B THR* 1.3 84.5 + - - +
247B VAL* 1.3 59.2 + - + +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 3.3 22.6 + - - +
150B MET 4.0 6.5 - - - +
152B GLU* 4.7 13.7 - - + -
155B ALA* 3.6 27.1 - - + -
243B LEU* 3.2 26.1 + - + +
244B TYR* 3.8 4.7 - - - +
246B LEU* 1.3 77.1 - - + +
248B SER* 1.3 61.3 + - - +
275B TYR* 3.3 10.6 - - + -
276B MET* 3.4 31.4 - - + -
280B CYS* 3.9 18.6 - - - -
284B LEU* 5.4 0.4 - - + -
306B TRP* 4.4 6.1 - - + -
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 3.7 8.8 - - - +
244B TYR* 2.9 39.8 + - - -
247B VAL* 1.3 79.5 - - - +
249B GLY* 1.3 61.9 + - - +
250B SER* 2.7 31.9 + - - -
273B PRO* 4.3 9.4 - - - -
275B TYR* 3.3 22.2 + - - -
276B MET* 4.9 0.7 - - - -
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 4.8 9.1 - - - -
144B LEU* 4.6 16.9 - - - +
145B VAL* 5.5 4.0 - - - +
148B GLY* 4.9 1.1 - - - -
149B ARG* 3.7 19.3 - - - +
245B THR* 2.8 22.3 + - - -
247B VAL 3.6 1.0 - - - -
248B SER* 1.3 79.5 - - - +
250B SER* 1.3 58.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il